To 2.:
Splunk 6.3 includes several improvements to PDF export around the ability to customize the output to match various branding and/or information guidelines. You will find them at Settings -> Server settings -> Email Settings.
I'm not sure what you mean by formatting the chart type...can you please be more specific? There is extensive material about chart configuration in the Splunk Data Visualizations Manual
As far as customizing the app logo in the PDF footer--you can hide it, but I don't think you can replace it. Quoting from the docs: "The reportIncludeSplunkLogo parameter for alert_actions.conf controls whether the Splunk logo appears in the PDF footers. It is set to 1 (true) by default. If you don't want to see the Splunk logo in your PDFs, set the value to 0 (false)."